Magnesium in PDB 8tjx: Tetrahymena Ribozyme Cryo-Em Scaffold

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Tetrahymena Ribozyme Cryo-Em Scaffold (pdb code 8tjx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Tetrahymena Ribozyme Cryo-Em Scaffold, PDB code: 8tjx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:56.1 occ:0.77 N7 N:G267 3.5 56.6 1.0 O6 N:G267 3.6 56.6 1.0 O6 N:G266 3.9 52.7 1.0 C6 N:G266 4.1 52.7 1.0 N7 N:G266 4.2 52.7 1.0 C5 N:G267 4.2 56.6 1.0 C6 N:G267 4.2 56.6 1.0 C5 N:G266 4.2 52.7 1.0 O6 N:G268 4.4 65.2 1.0 C8 N:G267 4.5 56.6 1.0 N7 N:G268 4.7 65.2 1.0 C8 N:G266 5.0 52.7 1.0 N1 N:G266 5.0 52.7 1.0

Magnesium binding site 2 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:67.6 occ:1.00 OP2 N:C32 2.2 51.4 1.0 OP1 N:A363 2.3 77.8 1.0 P N:C32 3.5 51.4 1.0 O5' N:C32 3.5 51.4 1.0 P N:A363 3.7 77.8 1.0 OP2 N:A33 3.7 50.0 1.0 O3' N:A362 4.2 78.0 1.0 C3' N:A31 4.3 49.4 1.0 O3' N:A31 4.3 49.4 1.0 OP2 N:A363 4.6 77.8 1.0 O2 N:U75 4.6 56.6 1.0 O5' N:A363 4.6 77.8 1.0 OP1 N:C32 4.6 51.4 1.0 C5' N:A363 4.8 77.8 1.0 C5' N:C32 4.9 51.4 1.0

Magnesium binding site 3 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:79.6 occ:0.87 OP2 N:A270 3.7 81.8 1.0 O6 N:G272 3.7 86.5 1.0 N7 N:A271 3.8 86.2 1.0 O4 N:U361 4.1 79.0 1.0 OP2 N:A271 4.3 86.2 1.0 O6 N:G273 4.5 84.2 1.0 N7 N:G272 4.5 86.5 1.0 N6 N:A271 4.5 86.2 1.0 C6 N:G272 4.6 86.5 1.0 C8 N:A271 4.7 86.2 1.0 C2 N:A362 4.7 78.0 1.0 P N:A270 4.7 81.8 1.0 O5' N:A270 4.8 81.8 1.0 C5 N:A271 4.8 86.2 1.0 N4 N:C360 4.8 78.0 1.0 N1 N:A362 4.9 78.0 1.0 C5 N:G272 5.0 86.5 1.0

Magnesium binding site 4 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:51.3 occ:0.78 OP1 N:A340 1.9 49.1 1.0 OP2 N:A343 1.9 54.1 1.0 OP1 N:A342 2.0 48.1 1.0 OP2 N:G344 2.5 51.2 1.0 P N:A340 3.3 49.1 1.0 P N:A342 3.3 48.1 1.0 P N:A343 3.4 54.1 1.0 P N:G344 3.8 51.2 1.0 OP2 N:A342 3.8 48.1 1.0 C5' N:A343 3.8 54.1 1.0 OP2 N:A340 4.0 49.1 1.0 O5' N:A343 4.1 54.1 1.0 C3' N:A342 4.1 48.1 1.0 O5' N:A342 4.1 48.1 1.0 O3' N:A339 4.1 48.0 1.0 OP1 N:G344 4.2 51.2 1.0 O3' N:A342 4.2 48.1 1.0 O5' N:A340 4.3 49.1 1.0 OP1 N:A343 4.3 54.1 1.0 O3' N:U341 4.4 53.5 1.0 C5' N:A342 4.5 48.1 1.0 O3' N:A343 4.5 54.1 1.0 C4' N:A343 4.6 54.1 1.0 OP1 N:A339 4.6 48.0 1.0 C4' N:U341 4.6 53.5 1.0 C3' N:U341 4.8 53.5 1.0 C4' N:A342 4.9 48.1 1.0 C5' N:U341 4.9 53.5 1.0 C5' N:A340 5.0 49.1 1.0

Magnesium binding site 5 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:48.0 occ:0.85 OP1 N:A339 2.1 48.0 1.0 OP2 N:A342 2.2 48.1 1.0 OP2 N:A340 2.3 49.1 1.0 P N:A339 3.4 48.0 1.0 P N:A342 3.7 48.1 1.0 P N:A340 3.7 49.1 1.0 N7 N:A340 4.0 49.1 1.0 OP2 N:A339 4.0 48.0 1.0 O5' N:A339 4.2 48.0 1.0 C8 N:A340 4.3 49.1 1.0 C3' N:A339 4.4 48.0 1.0 OP1 N:A340 4.4 49.1 1.0 O3' N:U341 4.5 53.5 1.0 N7 N:A342 4.5 48.1 1.0 O3' N:U338 4.5 48.4 1.0 OP1 N:A342 4.5 48.1 1.0 O5' N:A342 4.6 48.1 1.0 C3' N:U341 4.6 53.5 1.0 O3' N:A339 4.6 48.0 1.0 O5' N:A340 4.6 49.1 1.0 C8 N:A342 4.6 48.1 1.0 C5' N:A339 4.9 48.0 1.0 N3 N:A295 5.0 48.2 1.0

Magnesium binding site 6 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:43.8 occ:0.81 O6 N:G344 2.0 51.2 1.0 C6 N:G344 3.2 51.2 1.0 OP1 N:C321 3.8 48.0 1.0 C5 N:G344 4.1 51.2 1.0 OP2 N:A339 4.1 48.0 1.0 N1 N:G344 4.2 51.2 1.0 OP1 N:C322 4.2 49.3 1.0 OP2 N:C322 4.2 49.3 1.0 OP1 N:U324 4.2 52.9 1.0 N7 N:G344 4.3 51.2 1.0 OP2 N:U324 4.3 52.9 1.0 N7 N:A339 4.3 48.0 1.0 OP1 N:U338 4.4 48.4 1.0 C8 N:A339 4.4 48.0 1.0 P N:C322 4.6 49.3 1.0 C5' N:C321 4.6 48.0 1.0 P N:U324 4.8 52.9 1.0 O3' N:C321 4.9 48.0 1.0 C5 N:U324 4.9 52.9 1.0 P N:C321 5.0 48.0 1.0 C5' N:U338 5.0 48.4 1.0 O5' N:A339 5.0 48.0 1.0

Magnesium binding site 7 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:46.0 occ:0.84 N7 N:G319 2.1 49.4 1.0 O6 N:G320 2.7 48.6 1.0 C8 N:G319 2.8 49.4 1.0 C5 N:G319 3.3 49.4 1.0 C6 N:G320 3.5 48.6 1.0 OP2 N:G319 3.8 49.4 1.0 N7 N:G320 3.8 48.6 1.0 C5 N:G320 4.0 48.6 1.0 N9 N:G319 4.0 49.4 1.0 O6 N:G319 4.0 49.4 1.0 C6 N:G319 4.1 49.4 1.0 C4 N:G319 4.3 49.4 1.0 C5 N:U318 4.3 52.2 1.0 OP2 N:U318 4.4 52.2 1.0 C6 N:U318 4.5 52.2 1.0 N1 N:G320 4.6 48.6 1.0 O5' N:G319 4.6 49.4 1.0 O5' N:U318 4.7 52.2 1.0 N7 N:A334 4.8 55.1 1.0 P N:G319 4.8 49.4 1.0 C4 N:U318 4.9 52.2 1.0 N6 N:A334 4.9 55.1 1.0 O2 N:U333 4.9 54.9 1.0 O2' N:U333 4.9 54.9 1.0 C3' N:U318 5.0 52.2 1.0

Magnesium binding site 8 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:68.7 occ:0.78 O4 N:U318 3.9 52.2 1.0 N7 N:A317 3.9 56.9 1.0 N7 N:G316 4.4 61.1 1.0 N6 N:A317 4.4 56.9 1.0 C8 N:A317 4.8 56.9 1.0 C4 N:U318 4.8 52.2 1.0 C5 N:A317 4.9 56.9 1.0 OP1 N:A295 4.9 48.2 1.0 C8 N:G316 5.0 61.1 1.0

Magnesium binding site 9 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:68.8 occ:0.80 O6 N:G304 2.0 67.8 1.0 N7 N:G304 2.1 67.8 1.0 C6 N:G304 2.4 67.8 1.0 C5 N:G304 2.5 67.8 1.0 C8 N:G304 3.4 67.8 1.0 O6 N:G305 3.7 66.3 1.0 N7 N:G305 3.7 66.3 1.0 O6 N:G303 3.8 68.8 1.0 C4 N:G304 3.8 67.8 1.0 N1 N:G304 3.8 67.8 1.0 C6 N:G303 4.0 68.8 1.0 C6 N:G305 4.2 66.3 1.0 C5 N:G305 4.2 66.3 1.0 C5 N:G303 4.2 68.8 1.0 N9 N:G304 4.2 67.8 1.0 N7 N:G303 4.3 68.8 1.0 O4 N:U311 4.7 65.0 1.0 C8 N:G305 4.7 66.3 1.0 N1 N:G303 4.7 68.8 1.0 C2 N:G304 4.8 67.8 1.0 N3 N:G304 4.8 67.8 1.0 N3 N:U311 4.9 65.0 1.0

Magnesium binding site 10 out of 27 in the Tetrahymena Ribozyme Cryo-Em Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tetrahymena Ribozyme Cryo-Em Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:68.9 occ:0.87 OP2 N:G305 2.0 66.3 1.0 P N:G305 3.2 66.3 1.0 O5' N:G305 3.3 66.3 1.0 OP1 N:G305 4.1 66.3 1.0 C8 N:G305 4.1 66.3 1.0 N7 N:G306 4.2 66.1 1.0 OP2 N:G306 4.2 66.1 1.0 N7 N:G305 4.3 66.3 1.0 O3' N:G304 4.4 67.8 1.0 C3' N:G304 4.6 67.8 1.0 C5' N:G305 4.7 66.3 1.0 C8 N:G306 4.8 66.1 1.0 C3' N:G305 5.0 66.3 1.0

C.J.Langeberg, J.S.Kieft. A Generalizable Scaffold-Based Approach For Structure Determination of Rnas By Cryo-Em. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37791881
DOI: 10.1093/NAR/GKAD784